Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: K3863

Calculation Name: 2QC7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QC7

Chain ID: A

ChEMBL ID:

UniProt ID: P30040

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2542633.656705
FMO2-HF: Nuclear repulsion 2454737.976567
FMO2-HF: Total energy -87895.680138
FMO2-MP2: Total energy -88154.035451


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:33:VAL)


Summations of interaction energy for fragment #1(A:33:VAL)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-2.260.343-0.014-1.334-1.2550.007
Interaction energy analysis for fragmet #1(A:33:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.003
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A35THR0-0.037-0.0063.538-1.1401.463-0.014-1.334-1.2550.007
4A36LYS10.7650.8616.4250.3510.3510.0000.0000.0000.000
5A37GLY00.0600.0267.9430.1370.1370.0000.0000.0000.000
6A38ALA00.0010.0179.0880.0490.0490.0000.0000.0000.000
7A39LEU00.003-0.0079.492-0.144-0.1440.0000.0000.0000.000
8A40PRO00.017-0.0037.8300.1380.1380.0000.0000.0000.000
9A41LEU0-0.0040.00710.4460.1740.1740.0000.0000.0000.000
10A42ASP-1-0.767-0.86513.239-0.557-0.5570.0000.0000.0000.000
11A43THR0-0.007-0.03015.0590.0230.0230.0000.0000.0000.000
12A44VAL0-0.036-0.01017.8030.0480.0480.0000.0000.0000.000
13A45THR0-0.060-0.04815.1120.0290.0290.0000.0000.0000.000
14A46PHE00.026-0.00217.0800.0300.0300.0000.0000.0000.000
15A47TYR00.0100.01118.5400.0200.0200.0000.0000.0000.000
16A48LYS10.9220.95420.7850.2720.2720.0000.0000.0000.000
17A49VAL00.0100.00817.6430.0280.0280.0000.0000.0000.000
18A50ILE00.0570.03619.3900.0190.0190.0000.0000.0000.000
19A51PRO00.005-0.00222.5430.0150.0150.0000.0000.0000.000
20A52LYS10.7930.89822.8090.2500.2500.0000.0000.0000.000
21A53SER0-0.0100.00321.7810.0060.0060.0000.0000.0000.000
22A54LYS10.8190.90624.1620.1550.1550.0000.0000.0000.000
23A55PHE00.0470.02123.8720.0050.0050.0000.0000.0000.000
24A56VAL00.0350.01418.648-0.019-0.0190.0000.0000.0000.000
25A57LEU0-0.043-0.02717.8710.0220.0220.0000.0000.0000.000
26A58VAL0-0.012-0.00115.759-0.065-0.0650.0000.0000.0000.000
27A59LYS10.7980.8899.2621.1621.1620.0000.0000.0000.000
28A60PHE00.0010.00113.368-0.108-0.1080.0000.0000.0000.000
29A61ASP-1-0.724-0.89811.350-0.636-0.6360.0000.0000.0000.000
30A62THR0-0.015-0.01110.606-0.017-0.0170.0000.0000.0000.000
31A63GLN0-0.0020.0038.310-0.355-0.3550.0000.0000.0000.000
32A64TYR0-0.029-0.0185.151-0.039-0.0390.0000.0000.0000.000
33A65PRO00.0020.0206.5340.3100.3100.0000.0000.0000.000
34A66TYR0-0.034-0.0337.351-0.004-0.0040.0000.0000.0000.000
35A67GLY00.0560.0329.6920.0150.0150.0000.0000.0000.000
36A68GLU-1-0.834-0.92012.223-0.205-0.2050.0000.0000.0000.000
37A69LYS10.9460.95813.6230.1800.1800.0000.0000.0000.000
38A70GLN00.0700.0386.4240.1680.1680.0000.0000.0000.000
39A71ASP-1-0.867-0.93610.569-0.208-0.2080.0000.0000.0000.000
40A72GLU-1-0.788-0.87911.577-0.173-0.1730.0000.0000.0000.000
41A73PHE00.0040.0069.5860.0510.0510.0000.0000.0000.000
42A74LYS10.7960.8837.1180.2030.2030.0000.0000.0000.000
43A75ARG10.7870.86610.3920.1790.1790.0000.0000.0000.000
44A76LEU00.0190.00013.6620.0340.0340.0000.0000.0000.000
45A77ALA00.0320.03411.2950.0360.0360.0000.0000.0000.000
46A78GLU-1-0.856-0.90610.289-0.154-0.1540.0000.0000.0000.000
47A79ASN0-0.047-0.03813.7790.0650.0650.0000.0000.0000.000
48A80SER0-0.017-0.00115.2380.0180.0180.0000.0000.0000.000
49A81ALA0-0.070-0.04215.3520.0240.0240.0000.0000.0000.000
50A82SER0-0.052-0.02117.2470.0330.0330.0000.0000.0000.000
51A83SER0-0.002-0.01920.7390.0130.0130.0000.0000.0000.000
52A84ASP-1-0.916-0.93121.478-0.185-0.1850.0000.0000.0000.000
53A85ASP-1-0.864-0.93622.633-0.193-0.1930.0000.0000.0000.000
54A86LEU0-0.070-0.03519.547-0.012-0.0120.0000.0000.0000.000
55A87LEU00.0220.02315.764-0.018-0.0180.0000.0000.0000.000
56A88VAL0-0.0230.00414.0170.0150.0150.0000.0000.0000.000
57A89ALA0-0.024-0.00913.078-0.070-0.0700.0000.0000.0000.000
58A90GLU-1-0.853-0.9487.820-1.979-1.9790.0000.0000.0000.000
59A91VAL0-0.0280.00311.533-0.057-0.0570.0000.0000.0000.000
60A92GLY00.0600.0279.309-0.010-0.0100.0000.0000.0000.000
61A93ILE0-0.039-0.01410.3260.0490.0490.0000.0000.0000.000
62A94SER0-0.017-0.02012.0970.0000.0000.0000.0000.0000.000
63A95ASP-1-0.797-0.89114.057-0.145-0.1450.0000.0000.0000.000
64A96TYR0-0.054-0.02315.5980.0270.0270.0000.0000.0000.000
65A97GLY0-0.012-0.00416.844-0.014-0.0140.0000.0000.0000.000
66A98ASP-1-0.901-0.93616.703-0.123-0.1230.0000.0000.0000.000
67A99LYS10.8840.92516.8510.1830.1830.0000.0000.0000.000
68A100LEU00.0310.00711.478-0.026-0.0260.0000.0000.0000.000
69A101ASN00.0090.00612.5580.0260.0260.0000.0000.0000.000
70A102MET00.0960.05116.3160.0000.0000.0000.0000.0000.000
71A103GLU-1-0.812-0.89818.795-0.246-0.2460.0000.0000.0000.000
72A104LEU0-0.051-0.02416.7300.0120.0120.0000.0000.0000.000
73A105SER00.0390.02319.3080.0030.0030.0000.0000.0000.000
74A106GLU-1-0.953-0.97420.875-0.170-0.1700.0000.0000.0000.000
75A107LYS10.7840.88523.1000.2100.2100.0000.0000.0000.000
76A108TYR0-0.136-0.10321.5640.0110.0110.0000.0000.0000.000
77A109LYS11.0170.99823.2270.1330.1330.0000.0000.0000.000
78A110LEU0-0.040-0.00119.661-0.004-0.0040.0000.0000.0000.000
79A111ASP-1-0.837-0.89922.395-0.168-0.1680.0000.0000.0000.000
80A112LYS10.8130.87417.1880.1580.1580.0000.0000.0000.000
81A113GLU-1-1.001-0.99319.298-0.121-0.1210.0000.0000.0000.000
82A114SER0-0.014-0.02820.9060.0110.0110.0000.0000.0000.000
83A115TYR0-0.0840.00215.123-0.034-0.0340.0000.0000.0000.000
84A116PRO0-0.067-0.05114.2050.0310.0310.0000.0000.0000.000
85A117VAL00.0400.01016.0170.0490.0490.0000.0000.0000.000
86A118PHE0-0.044-0.01315.221-0.056-0.0560.0000.0000.0000.000
87A119TYR00.0190.00419.3050.0440.0440.0000.0000.0000.000
88A120LEU0-0.006-0.01120.916-0.033-0.0330.0000.0000.0000.000
89A121PHE0-0.029-0.00920.5870.0220.0220.0000.0000.0000.000
90A122ARG10.9040.92824.3900.1520.1520.0000.0000.0000.000
91A123ASP-1-0.820-0.91527.330-0.150-0.1500.0000.0000.0000.000
92A124GLY0-0.0210.00026.4130.0100.0100.0000.0000.0000.000
93A125ASP-1-0.819-0.88727.457-0.162-0.1620.0000.0000.0000.000
94A126PHE00.0360.00623.163-0.019-0.0190.0000.0000.0000.000
95A127GLU-1-0.864-0.91026.501-0.173-0.1730.0000.0000.0000.000
96A128ASN0-0.107-0.05128.9180.0140.0140.0000.0000.0000.000
97A129PRO0-0.0340.01624.4280.0010.0010.0000.0000.0000.000
98A130VAL00.0530.01926.4700.0070.0070.0000.0000.0000.000
99A131PRO00.0130.02124.070-0.023-0.0230.0000.0000.0000.000
100A132TYR0-0.028-0.01621.2260.0250.0250.0000.0000.0000.000
101A133THR00.000-0.01023.315-0.012-0.0120.0000.0000.0000.000
102A134GLY00.0070.00624.4450.0180.0180.0000.0000.0000.000
103A135ALA00.0230.00822.563-0.003-0.0030.0000.0000.0000.000
104A136VAL00.0140.02216.984-0.005-0.0050.0000.0000.0000.000
105A137LYS10.9340.96818.3160.1170.1170.0000.0000.0000.000
106A138VAL00.0520.01716.8940.0010.0010.0000.0000.0000.000
107A139GLY0-0.052-0.02519.5460.0040.0040.0000.0000.0000.000
108A140ALA0-0.081-0.04022.8710.0040.0040.0000.0000.0000.000
109A141ILE00.0880.04218.1300.0080.0080.0000.0000.0000.000
110A142GLN00.0670.02520.131-0.006-0.0060.0000.0000.0000.000
111A143ARG10.9330.97023.2960.1200.1200.0000.0000.0000.000
112A144TRP00.0310.02023.1270.0010.0010.0000.0000.0000.000
113A145LEU00.0560.03920.9510.0010.0010.0000.0000.0000.000
114A146LYS10.9050.95025.3340.1550.1550.0000.0000.0000.000
115A147GLY0-0.051-0.02528.0260.0080.0080.0000.0000.0000.000
116A148GLN0-0.106-0.04027.3640.0090.0090.0000.0000.0000.000
117A149GLY00.0050.00029.478-0.003-0.0030.0000.0000.0000.000
118A150VAL0-0.020-0.01424.224-0.009-0.0090.0000.0000.0000.000
119A151TYR0-0.034-0.01226.3850.0120.0120.0000.0000.0000.000
120A152LEU0-0.018-0.00722.120-0.009-0.0090.0000.0000.0000.000
121A153GLY0-0.0020.00124.8760.0110.0110.0000.0000.0000.000
122A154MET0-0.005-0.01623.444-0.012-0.0120.0000.0000.0000.000
123A155PRO00.0380.01419.4270.0070.0070.0000.0000.0000.000
124A156GLY0-0.018-0.01021.4230.0140.0140.0000.0000.0000.000
125A157CYS0-0.048-0.00322.7880.0110.0110.0000.0000.0000.000
126A158LEU00.008-0.00124.711-0.009-0.0090.0000.0000.0000.000
127A159PRO00.1040.06827.9370.0090.0090.0000.0000.0000.000
128A160VAL00.0230.01730.7480.0040.0040.0000.0000.0000.000
129A161TYR0-0.041-0.06630.0820.0070.0070.0000.0000.0000.000
130A162ASP-1-0.868-0.91629.748-0.067-0.0670.0000.0000.0000.000
131A163ALA0-0.045-0.02432.7390.0030.0030.0000.0000.0000.000
132A164LEU00.007-0.00135.0670.0040.0040.0000.0000.0000.000
133A165ALA00.0150.02334.4250.0040.0040.0000.0000.0000.000
134A166GLY00.0460.01736.5140.0030.0030.0000.0000.0000.000
135A167GLU-1-0.966-1.00538.826-0.034-0.0340.0000.0000.0000.000
136A168PHE0-0.017-0.03139.1570.0030.0030.0000.0000.0000.000
137A169ILE0-0.062-0.02139.5410.0020.0020.0000.0000.0000.000
138A170ARG10.8960.96241.0040.0380.0380.0000.0000.0000.000
139A171ALA0-0.063-0.01444.4380.0010.0010.0000.0000.0000.000
140A172SER00.0430.01646.3730.0010.0010.0000.0000.0000.000
141A173GLY00.0290.02547.1880.0000.0000.0000.0000.0000.000
142A174VAL0-0.073-0.05047.5970.0000.0000.0000.0000.0000.000
143A175GLU-1-0.804-0.92746.538-0.018-0.0180.0000.0000.0000.000
144A176ALA00.0810.06543.393-0.001-0.0010.0000.0000.0000.000
145A177ARG10.9890.97142.6040.0100.0100.0000.0000.0000.000
146A178GLN0-0.035-0.01342.858-0.001-0.0010.0000.0000.0000.000
147A179ALA00.0200.01940.539-0.001-0.0010.0000.0000.0000.000
148A180LEU0-0.004-0.01237.014-0.001-0.0010.0000.0000.0000.000
149A181LEU0-0.023-0.01338.4170.0000.0000.0000.0000.0000.000
150A182LYS10.9050.96337.6290.0360.0360.0000.0000.0000.000
151A183GLN0-0.013-0.01234.7510.0000.0000.0000.0000.0000.000
152A184GLY00.0300.01234.130-0.002-0.0020.0000.0000.0000.000
153A185GLN0-0.046-0.02735.276-0.001-0.0010.0000.0000.0000.000
154A186ASP-1-0.820-0.88232.416-0.052-0.0520.0000.0000.0000.000
155A187ASN00.0030.00729.039-0.002-0.0020.0000.0000.0000.000
156A188LEU0-0.072-0.01529.818-0.003-0.0030.0000.0000.0000.000
157A189SER0-0.008-0.02030.666-0.002-0.0020.0000.0000.0000.000
158A190SER0-0.074-0.05526.484-0.005-0.0050.0000.0000.0000.000
159A191VAL00.0310.02823.6700.0020.0020.0000.0000.0000.000
160A192LYS10.8900.94916.8260.1410.1410.0000.0000.0000.000
161A193GLU-1-0.737-0.85320.162-0.026-0.0260.0000.0000.0000.000
162A194THR0-0.110-0.05816.9280.0120.0120.0000.0000.0000.000
163A195GLN00.0780.00019.2520.0170.0170.0000.0000.0000.000
164A196LYS10.9080.96821.7660.0360.0360.0000.0000.0000.000
165A197LYS10.8670.92518.1260.0030.0030.0000.0000.0000.000
166A198TRP0-0.024-0.02118.1140.0010.0010.0000.0000.0000.000
167A199ALA00.0830.05524.8740.0010.0010.0000.0000.0000.000
168A200GLU-1-0.877-0.94727.152-0.015-0.0150.0000.0000.0000.000
169A201GLN00.0300.02624.5680.0010.0010.0000.0000.0000.000
170A202TYR00.033-0.01127.4500.0020.0020.0000.0000.0000.000
171A203LEU00.0840.03631.0770.0040.0040.0000.0000.0000.000
172A204LYS10.8630.92330.1880.0040.0040.0000.0000.0000.000
173A205ILE0-0.065-0.02530.0180.0030.0030.0000.0000.0000.000
174A206MET0-0.0150.00433.9450.0000.0000.0000.0000.0000.000
175A207GLY00.011-0.00236.9040.0010.0010.0000.0000.0000.000
176A208LYS10.8900.95931.4450.0030.0030.0000.0000.0000.000
177A209ILE0-0.082-0.02337.2690.0010.0010.0000.0000.0000.000
178A210LEU0-0.080-0.03840.1050.0000.0000.0000.0000.0000.000
179A211ASP-1-0.935-0.94540.2550.0020.0020.0000.0000.0000.000
180A212GLN0-0.076-0.04238.071-0.001-0.0010.0000.0000.0000.000
181A213GLY00.1150.04942.1870.0010.0010.0000.0000.0000.000
182A214GLU-1-0.907-0.95441.879-0.015-0.0150.0000.0000.0000.000
183A215ASP-1-0.927-0.94541.706-0.016-0.0160.0000.0000.0000.000
184A216PHE0-0.0140.00934.3640.0020.0020.0000.0000.0000.000
185A217PRO00.0440.02035.5430.0010.0010.0000.0000.0000.000
186A218ALA00.0250.00335.5920.0010.0010.0000.0000.0000.000
187A219SER0-0.008-0.00936.5390.0000.0000.0000.0000.0000.000
188A220GLU-1-0.747-0.86532.0590.0040.0040.0000.0000.0000.000
189A221MET00.0060.01531.5430.0010.0010.0000.0000.0000.000
190A222THR0-0.035-0.02331.686-0.002-0.0020.0000.0000.0000.000
191A223ARG10.7980.88628.739-0.007-0.0070.0000.0000.0000.000
192A224ILE00.001-0.01726.2110.0050.0050.0000.0000.0000.000
193A225ALA00.0430.03227.5760.0000.0000.0000.0000.0000.000
194A226ARG10.9250.97428.7780.0030.0030.0000.0000.0000.000
195A227LEU0-0.020-0.00225.8320.0020.0020.0000.0000.0000.000
196A228ILE00.0370.01823.1390.0080.0080.0000.0000.0000.000
197A229GLU-1-0.916-0.94824.327-0.019-0.0190.0000.0000.0000.000
198A230LYS10.8350.90025.836-0.010-0.0100.0000.0000.0000.000
199A231ASN00.0420.03820.5180.0030.0030.0000.0000.0000.000
200A232LYS10.9430.98821.717-0.050-0.0500.0000.0000.0000.000
201A233MET0-0.081-0.04319.7280.0030.0030.0000.0000.0000.000
202A234SER00.0150.00714.222-0.013-0.0130.0000.0000.0000.000
203A235ASP-1-0.714-0.86113.033-0.078-0.0780.0000.0000.0000.000
204A236GLY0-0.0030.01113.455-0.024-0.0240.0000.0000.0000.000
205A237LYS10.9440.96414.106-0.144-0.1440.0000.0000.0000.000
206A238LYS10.9440.97117.2790.0030.0030.0000.0000.0000.000
207A239GLU-1-0.783-0.86715.875-0.118-0.1180.0000.0000.0000.000
208A240GLU-1-0.887-0.94017.2680.0050.0050.0000.0000.0000.000
209A241LEU0-0.075-0.04019.6200.0020.0020.0000.0000.0000.000
210A242GLN00.0190.01120.6170.0000.0000.0000.0000.0000.000
211A243LYS10.8660.92817.0040.1100.1100.0000.0000.0000.000
212A244SER00.016-0.01022.8380.0010.0010.0000.0000.0000.000
213A245LEU0-0.097-0.04625.3670.0020.0020.0000.0000.0000.000
214A246ASN00.0500.00423.1400.0040.0040.0000.0000.0000.000
215A247ILE0-0.042-0.00125.1570.0010.0010.0000.0000.0000.000
216A248LEU00.007-0.01828.6680.0020.0020.0000.0000.0000.000
217A249THR0-0.093-0.05130.2200.0010.0010.0000.0000.0000.000
218A250ALA00.0040.00931.8210.0000.0000.0000.0000.0000.000
219A251PHE0-0.008-0.01232.3720.0020.0020.0000.0000.0000.000
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